Return Home
by Deliwiel
Summary: What if John made it off the roof before the missile hit? Why hasn't he contacted his friends?
1. Chapter 1

_Disclaimer: I do not own POI, or the characters. Otherwise I would have ended things differently... *Sniffs* anyhow...enjoy!_

John spared every second he wasn't firing at Samaritan ops to check on Finch and make sure he got off the roof safely. As soon as he made sure the other door had closed and his friend was out of danger he turned his full attention back to the matter at hand-namely the people that were firing at him and trying to stop the upload of The Machine to the satellite.

He heard her in his ear, but it was strange; it almost felt like she was a physical form, standing right beside him, supporting him. He continued in the bullet exchange for a few more moments before feeling a fiery-hot pain rip through his shoulder. He fell to his knees with a grunt, but forced himself back up. He got a few more shots out before he felt another bit of fire enter his gut, and another one in his leg. He fell again, only this time, he wasn't able to make it back to his feet. He continued firing his weapon though, making sure no one would get near the briefcase. His vision started swimming in front of him, but he forced himself to keep firing, discharging bullet after bullet, until finally the last operative that he could see was on the ground.

"It's done," Root's voice chimed in his ear. He felt a burden lifted off his shoulders, and he smiled in triumph. His smile was replaced by a grimace though as the adrenaline started to wear off and he felt all the pain and agony those bullets had caused. "It'll all be over soon, though," he thought to himself.

"Can you hear me?" he asked quietly, hoping to hear the voice of The Machine one more time, but all he got was white noise. He felt nothing but the numbness in his hands and heard nothing but the static in his mind as he struggled to sit up. He glanced around, trying to determine how long it would take before the missile arrived. He couldn't see or hear any sign of it, but he knew it was coming, and that it wouldn't be long.

He didn't know what made him do it, but he forced himself to his feet and, using the ledge for support, made his way around the roof towards the door leading back inside. He barely made it twenty feet before he fell to his knees with a grunt of pain. Looking down at his shirt, he saw that the entire front was covered in red. There wasn't a speck of white left visible to his eye. He started crawling towards the door, supporting himself on his good arm, but before he got far, the door burst open and half a dozen figures in black converged on the roof, moving towards him at a rapid pace, guns trained on him.

He shook his head to clear the cobwebs, then raised his own gun while still on his hands and knees and pulled the trigger. The first shot clipped one of them in the arm, spinning the man around and leaving him crying in pain, while the second bullet that exited from the chamber nailed the target in the upper thigh, dropping him. He pulled the trigger a third time only to hear the empty click as his gun informed him that the magazine was empty. He tossed the gun away from him and tried to push himself back up into a standing position, but the remaining four hostiles surrounded him. He got ready to put up as much of a fight as he could, but the butt of one of their rifles quickly put a stop to that idea. He collapsed to the ground without a sound, lying on his stomach.

"Get him up and off the roof, quick!" said the man who had introduced John's face to the butt of his gun. "We've got less than two minutes before the missile hits." One of them bent down and picked up the ex-agent in the fireman's carry, then hurried as fast as he could to the door leading downstairs. He was flanked by two men who kept watch, guns trained and ready to fire at anything that moved. The one in charge stood over the two who had been hit by John's bullets. "Get up or stay and die," he commanded harshly before he followed the men carrying the unconscious John. The one who had been hit in the arm scrambled to his feet, but the man who had been shot in the leg was unable to get up on his own. He called out for help, but his companion simply gave him a pitiful look and hurried through the door. He heard through the com link the harsh commands to get the ex-CIA agent in the car, and then he heard the sound of a car peeling away from the building. He had barely registered those sounds when a new sound entered into his ears; the sound of a drone. One tear slipped down his cheek before his whole world exploded.

 _1 week after the final fight, Finch_

"Harold?" Grace asked as she stared at him, not wanting to believe her eyes.

"Hello, Grace," Finch replied. His voice was soft; he sounded like a man who had been broken, but he pushed that aside and continued to look at Grace.

"Wha-I don't understand...the bomb, the ferry…" she stuttered. Her hand went up and covered her mouth, slightly muffling her words. She stumbled back a bit as Harold walked towards her, and he stopped, not sure whether to keep moving forward or not. His answer came to him as Grace dropped her paint pallet and crossed the distance between the two of them, throwing her arms around him and burying her cheek into his shoulder. He grimaced and uttered a small cry of pain as his spinal injury acted up, his week-old bullet wound throwing in its complaints as well. Grace hastily pulled back. "I'm sorry, did I hurt you?" she asked, placing her hand lovingly on his cheek and scanning her eyes over him for his injuries. He felt his heart expand with love that he only felt while he was around this woman, placing his own hand over hers.

"You didn't hurt me, Grace. How can you think that when I'm the one that has so obviously been the cause of your pain?" Grace simply stared at him. He pulled her gently over to the closest table, sitting himself down next to her. "There are some things I was going to tell you before...well, before everything fell apart. If you want me to, I would still like to tell you those things now." Grace, still wide-eyed and obviously in shock, simply nodded, and Harold commenced telling her a story about a machine and a very special group of friends who worked to save people from violent crimes, sacrificing everything they had for their cause.

 _1 week after the final fight, Fusco_

Shaw had just left him in the diner, taking Bear with her. He grumbled a little bit, but knew that the dog would be happier with her. He also thought maybe she'd be a little less crazy if she had permanent ownership of the dog, but somehow he seriously doubted that. He left the money on the table to pay for his meal as well as his tip and slowly made his way out the door.

Shaw joked about the knife wounds not affecting his appetite, and she was probably right. What was affecting his appetite was not knowing what had happened to Glasses and Wonderboy. He had a gut feeling that he hoped was wrong, but years as a detective told him that usually his gut instinct was right. Currently his gut was telling him that one, maybe both of them, had not made it out alive. He shook his head, dispelling those thoughts. Until he had proof, he refused to give up on them. He just wished he knew where to start looking.

He walked into the precinct and ignored the stares that were coming his way. The captain had been removed of duty after taking a look at the security footage from when he and John had been apprehended, and he was given back his job. There was still going to be an investigation, but he had been informed that there wasn't anything substantial that would hold up in court against him or Det. Riley.

He sat at his desk and out of habit looked across at the desk where first Joss, then John used to sit. He was starting to think that that desk was cursed. He rubbed his face, trying to think about anything other than his missing partner. He turned to the stack of cases on his desk, deciding now was as good a time as any to dive back into his day job.

 _2 weeks after the final fight, Shaw_

Shaw grabbed her latest POI and they ducked behind a counter in the doctor's office. The latest number was a doctor who had accidentally stumbled into some loan sharks having a "discussion" with one of their clients, who had later ended up in the ER, where he passed away. The doctor had agreed to testify, but for some reason at the last minute decided not to.

She peered around the counter and fired three shots, taking down the approaching figures. They all groaned and rolled on the floor in pain while Shaw looked back to her ward. She gestured towards the door. "Alright, are you ready to get out of here?" she asked. He hastily nodded his head. "Let's go then," she continued as she pulled the man to his feet.

"Well done sweetie," Root's voice purred in her ear. Shaw ignored the voice as she focused on getting them both out the front door. "7 o'clock," The Machine informed her. Without looking, Shaw swiveled her arm back and shot the kneecap of the person trying to sneak up on her. The doctor looked at her.

"Who _are_ you?" he asked. Shaw sighed. They always asked that.

"Concerned third party," came her distracted reply. The doctor continued asking questions, but Shaw tuned him out as she turned to talk to The Machine. "Are there any more coming?"

"Just one; the big shark," replied the AI.

"Where?"

"He'll round that corner in thirty seconds." Shaw prepared herself and waited for the loan shark to show his face. She also pushed the doctor back to the wall opposite her so that he was out of sight of the man coming for him. She saw him turn the corner and pull a gun on her, but she was faster; before he could even pull his gun all the way out, he was down on the ground, clutching at his knees. Shaw walked over to him, kicking his fallen gun away from him. "I've gone ahead and alerted the authorities; they're on their way," The Machine informed her. Shaw smirked as she heard the sirens getting closer and closer. She pulled out a ziptie and bound the man's hands together, then turned and looked at the visibly shaken doctor.

"I think you can handle it from here, yeah?" she asked. "Just do me a favor and don't see any sketch artists to describe me. Tell them I was wearing a ski mask or something. Otherwise, I know where you work, and I know where you live." She gave him an evil eye before turning and jogging down the street mere seconds before the cop cars pulled up.

She entered the run-down apartment building she had called home for the past two weeks, sat on the broken couch and propped her feet up on the small table in front of her. After taking the earpiece out of her ear and tossing it on the table as well, she gave a short whistle and Bear came barreling out of the kitchen and hopped up next to her. She pet the enthusiastic Malinois and chuckled as he tried to lick her face. She thought about Fusco, hoping that his wounds were healing okay, and then her thoughts wandered to John and Finch. She only let herself think about them for a few seconds before shaking her head, pushing them out of her thoughts.

"Come on, Bear, wanna go for a walk?" The dog gave an excited bark and hopped off the couch, fetching his leash and pressing it into Shaw's hand. She chuckled again as they walked out the door, back into the streets of New York.

 _5 weeks after the final fight, Present Time, Finch_

"Harold?" Grace's voice broke through his thoughts as he was staring at the headstone in front of him. He glanced over at his once-again fiance, who was holding out a cup of tea for him. He accepted it with a small smile and put his arm around her as she came and stood by his side. "Is there anything that I can do?" He gave her another small smile, turning to stare into her gorgeous eyes.

"You can continue being you," he stated simply. She nodded in understanding and leaned her head on his shoulder.

"He sounds like he was an amazing person," she remarked. Harold nodded.

"He was. He was selfless and protective. He was the best friend anyone could have asked for." His voice shook slightly. It was still difficult, even after over a month.

There had been nothing left on the roof after the missile hit, but he knew that nothing up there would have survived, and there would have been no remains left. He had hacked the police database a few weeks ago and confirmed that there had been no testable remains left on the roof, but he knew whose remains they would have been. He had then decided to honor John and get him a better headstone than the one the CIA had given him after they thought he was killed in Ordos.

He and Grace stood there for a few more minutes before Harold finally stretched, then turned to the woman next to him. "Are you ready to go home?" he asked Grace. She looked up in his eyes, nodding.

"Yeah, I am. But only if you are," she insisted.

"I am," he smiled at her as they turned away and walked out of the cemetery. They travelled for a few minutes in silence before Grace looked up at Harold.

"What's wrong?" she asked.

"Hmm?"

"You look like you're deep in thought about something," she clarified.

"Ah. I was simply wondering what Ms. Shaw and Detective Fusco have been doing, if they're alright."

"Why can't you just contact them and ask?"

"I think Ms. Shaw wants to be left alone right now, and I don't want to endanger Detective Fusco anymore. He's been through enough the past few years. He deserves some well-earned time with his son. To have a life free of HR, Mr. Reese, me…" he trailed off. Grace put her hand on his arm.

"Are you sure that's what he would want?" Before Finch could answer, a figure in black leggings and a black jacket stepped out in front of them.

"Pretty sure it's not what he wants, but hey. Maybe I don't know him as well as you do," Shaw commented drily.

"Ms. Shaw?" Finch's mouth was open slightly in shock. Grace's eyes widened.

"Hey Finch. Long time no see."

"What are you doing here?"

"Well, I came to tell you that I think your machine is on the fritz, and I came to pay my respects to John." She brushed past him and walked back towards where Finch and Grace had just come from.

"Wha-my machine? What are you talking about, Ms. Shaw? The Machine was destroyed along with Samaritan!" Shaw shot him a slightly annoyed look as she stopped at the headstone.

"Nope. Somehow she got another copy of herself made and stored safely somewhere. She started calling me about a month ago, giving me numbers again. She's basically the same Machine. She even has the same...same voice." Her voice wavered a little bit, and Finch knew she was thinking about Root. She composed herself quickly and continued talking. "I would have come to you sooner, but I didn't know if you had survived or not, and the numbers kept coming. Thanks for letting us know you were okay, by the way," she added, voice dripping with sarcasm. Harold ignored the last comment.

"Even if all this were true, how did you find me?"

"About two weeks ago, The Machine alerted me that someone had hacked the NYPD database, only looking at one file; the one about the building that was hit with a missile. She told me it was you, and she told me where to find you."

"But if you knew for this long, why-"

"Wait to come find you?" She shrugged. "I was doing fine with the numbers, and once The Machine told me where you were, I did go look for you. I saw you'd found your way back to Grace, so I decided to let you have some space. Sounds like we all had the same idea," she added. Finch's head was still reeling.

"But why come now?" he finally asked.

"I told you, your machine is on the fritz, and you're the only one I trust to fix it."

"What makes you say it's on the fritz?" Shaw reached into her jacket pocket and handed Finch a folded piece of paper, then turned back to the headstone and stood there with her hands stuffed in her pockets. Finch unfolded the piece of paper and stared at what was scribbled there. The numbers seemed familiar…

"A number. Well it shouldn't come as a surprise to you, Ms. Shaw, but The Machine _is_ programmed to give out numbers of people who need assistance. There's nothing strange about that."

"Look closer at the number, Finch," Shaw instructed. He did as he was told. He couldn't shake the feeling that he knew those numbers…

"This...this is John's number!" he finally exclaimed.

"Bingo. Either your machine is a little behind the times, or it's completely delusional. Either way, it needs fixing. Will you help me?" Finch looked at her, then Grace, then back to Shaw.

"Ms. Shaw, I-"

"Harold." Grace put her hand on his cheek, making him look at her. "Go help her. The Machine is still out there, still giving you new numbers to save!"

"No, I can't, I'm done with that life, I-"

"Finch, I'm not asking you to become Watchtower. All I need is for you to come work some of your computer magic, get us working again." She stared at him, and after a few more moments of looking between the two women standing before him, Harold sighed.

"Alright. I'll see what I can do."

Shaw led Finch and Grace down an alley into an abandoned warehouse. "Lovely accommodations," Finch muttered to himself. An excited yelp had him turning around quickly as an excited Bear ran towards him. "Bear!" He reached down and pet the excited dog, whose tail continued to wag incessantly. Grace bent down as well, letting him sniff her hand before cautiously letting her rub his ears. Harold smiled a small smile before turning his attention back to the building they were in. It reminded him of his old Library, actually. Sitting in the middle of the warehouse was a large cabinet, and inside he could see blinking lights of different power sources. "That's The Machine?" he asked, pointing to it.

"Yup, what's left of her. Or at least what she needs to function at the moment. She says there's always room for improvement, but this will do for now." She gestured towards a desk with several monitors sitting on or around it. Finch gingerly sat himself down and began to type away, looking for any sort of error.

 _Several Hours Later_

"Ms. Shaw, I cannot find anything wrong with the code. This is quite perplexing," Finch admitted. Shaw shoved the rest of her donut in her mouth and walked over to stand behind him.

She had gone out to get some food and entertainment for everyone about an hour ago after realizing Grace was starting to get fidgety. Besides, Bear needed a walk. She had brought back a book and some coffee for Grace, donuts, as well as tea for Harold, and a massive bone that Bear was currently trying to devour.

"So….what? John's number has been used in identity theft?" Shaw was only half joking. She was still confused, but if Harold said The Machine was working… Harold looked into the webcam.

"Can you see me?"

::YES::

"Who am I?"

::HAROLD, ADMIN::

"Find Sameen Shaw."

::LOCATING PRIMARY ASSET…:: A yellow box appeared around Shaw's face on the monitor. Finch and Shaw shared a glance.

"Locate John Reese."

::LOCATING PRIMARY ASSET…LOCATION UNKNOWN::

"Why did you give Ms. Shaw Mr. Reese's number? What makes you think he is in danger?"

::ACCESSING AUDIO RECORDING….::

" _That's him? The great, feared, unbeatable Reese? Doesn't seem so scary to me!"_

" _He didn't put four guys in the hospital five minutes after he woke up," chided a second voice. "Even heavily sedated and drugged, this guy is dangerous. The boss wants him taken care of, but she wants to do it personally. We're supposed to wait for instructions, but she said we're gonna make our move soon. We're going to bring him to her, but first we need to take care of his arm. I'll keep you updated on the plan."_

::AUDIO RECORDING COMPLETE::

During the conversation, Shaw had moved closer to Finch, staring at the screen with a look of shock on her face.

"What day was this recorded?"

::JULY 15, 2016, 7:37 PM::

Finch checked his watch. That was less than 16 hours ago! "Do you have a video recording?" Shaw asked, trying to not sound excited. If this was some stupid glitch, she didn't want to have her hopes up for nothing.

::CAMERA ACCESS UNAVAILABLE::

She sighed in frustration.

"Can you show me footage of the building Mr. Reese was on, right before the explosion?" Finch asked.

::ACCESSING VIDEO RECORDING::

Finch, Shaw, and Grace watched the 5 minutes before the explosion, but they couldn't see anything on the roof. As the missile hit, Finch turned his head away and Grace put a supportive hand on his shoulder. "Nothing," Finch mumbled. He started to push the chair away from the desk, but Shaw stopped him.

"Hold on!" He gave her a look that clearly radiated disappointment, but she wasn't going to give up that easily. "Show us footage of a camera facing the front door of that building!"

::ACCESSING VIDEO RECORDING::

This time as they watched, they saw two black SUV's screech to a halt in front of the building. Six men poured out of them almost before they stopped, leaving only the drivers in the cars. Nothing happened for a few minutes, until suddenly the front doors burst open and five of the original six men came out. One was clutching at his shoulder, but the rest seemed to be crowded around one man who had someone on his back.

"Pause the video," Finch commanded. The AI complied. "Can you zoom in and enhance the image?" Once again, The Machine did as she was told. Finch sat back. There was no mistaking that suit, and as they had The Machine play the video in slow motion, when the unconscious man was thrown in the backseat of one of the vans, there was no doubt left in any of their minds. John Reese was alive, and he was in the hands of dangerous looking people. But if he was already taken by someone, who was talking about him over that recording?


	2. Chapter 2

_1 week after final fight_

Awareness came back to John slowly; a few sounds here and there, the feeling of sheets under him, sometimes he would feel a pinch on his arm. He tried opening his eyes to see where he was, but immediately shut them again. It was too bright. He tried again slowly, opening them a fraction of an inch at a time. Finally, when they were open all the way, he squinted, looking around the pristine white room.

He realized his suit was gone, replaced by a soft t-shirt and what felt like pajama pants. When he tried to move his left arm, he found it wouldn't cooperate. He sluggishly looked down and saw that his wrist and elbow were both velcroed to the hospital bed he was in. He looked to his right, expecting to see his other arm with the same treatment, but instead he saw that his right arm was in a sling, which was strapped tightly to his chest. He tried moving it, but the sling was extremely tight, and there was a sharp fire that ripped through his shoulder when he tried.

He couldn't stop the soft groan that escaped his lips. In a flood of memories, everything came back to him. The roof, Samaritan, the men in black… As he was struggling with the memories, the door to his room opened and a doctor in a lab coat walked in. He was followed by four more men in black, who took up defensive positions around the bed and by the door.

"Good to see you're finally awake," the doctor commented as he examined his papers. John said nothing, just continued to stare at him. "You came to me with multiple gunshot wounds, and you were in hypovolemic shock. We had to have you in a medically induced coma for the past week to help you heal." John started. A week? The doctor continued talking. "Can you tell me anything? How're you feeling? Pain level on a scale of 1-10?" As the stony silence continued, the doctor sighed impatiently. "Listen, I've got a lot I need to do today, but seeing as how you're my number one priority according to the boss, if you could just tell me if anything is wrong or not, I'll be on my way."

"Where do I start?" rasped John finally. "I was shot multiple times, beaten with a rifle, kidnapped, I'm strapped to a bed, and," he added as an afterthought, hoping it would work. "I can't feel my right arm." The doctor looked a little less frustrated at the last statement, moving closer to his patient.

"Well, there could be a number of reasons for that," he said thoughtfully as he examined John with a practiced eye. "You _were_ shot there. There may be some muscular or nerve damage that is causing the numbness." John raised an eyebrow.

"Is that your medical observation or are you simply stating the obvious?" The doctor bristled a little. John felt a small smile tug at his mouth, even though he knew the situation he was in hardly called for humor.

"Is it a tingling kind of numbness, or can you not feel anything, not move anything?"

"I can't feel anything." The doctor scrunched his forehead, then leaned over John towards his right side. As he started loosening the sling to check out his patient's arm, John gritted his teeth for the pain he knew was about to come.

As soon as the sling was loose enough, Reese ripped his right arm out of the sling completely and rammed his elbow into the doctor's face. Quick as lightning, he reached over and yanked on the velcro holding his elbow and wrist down, freeing up his left arm as well. The first of the men in black, the one who was closest to him, came at him, but a good kick to the gut sent him stumbling back, though not taking him out of the equation entirely. Reese lept off his bed, even though the bullet wound in his thigh begged him to stop moving. "Shoulda restrained my legs too, fellas," he commented in his soft voice.

The next op to get close enough to him was grabbed by John and spun around right as one of the remaining fighters fired his gun, hitting his comrade in the side instead of John. John tossed the shot man away from him, getting ready for hand-to-hand combat. Three against one. John knew if he hadn't been shot, he could have taken these guys down easy, but they had the advantage of his injuries.

The first man came at him, pulling a knife out of his belt and raising it to take a swipe at John. Reese pushed it out of the way with his right hand, only slightly wincing as he felt the blade slice through the flesh on his palm. He didn't pay much attention to it though as he delivered a left handed uppercut to his opponent, then finished him off with a solid kick in the ribs. The man crashed into and tumbled over a cart with syringes and medication, then fell to the floor in a heap.

One of the remaining two men jumped him from behind, putting his arms around John's neck. John gripped at the arms, futilely trying to pry them off his throat. The last man advanced slowly on John, gun trained and ready to fire. Reese seemingly relaxed, appearing to have given up. The man approached cautiously, while the one behind him kept a firm grip on John's neck. It wasn't tight enough to strangle him, but enough to make him behave. As the man in front drew nearer, with lightning fast reflexes Reese reached out and grabbed the handgun away from him with his left hand, firing with precision and hitting him in the kneecap. He then wrapped his left arm around the opposite side of his waist, pointed downward slightly and pulled the trigger, effectively eliminating the threat of being followed.

He quickly made his way towards the door, wanting to get far enough out of the building before the adrenaline wore off and his body reminded him that he had been shot. Multiple times. He jogged down the hallway and found a door leading to some stairs just as the alarm started to blare. He figured he had 30 seconds or less before he was discovered, which simply persuaded him to take the stairs two, sometimes three at a time until he reached the bottom level and burst through the door that read "Exit." He found himself outside in a small alley which he promptly left.

He stared up at a camera on a lightpole. "Can you hear me?" he asked, almost desperately. His heart sank as he realized there were no blinking lights, and the wires to the camera were hanging out in the open. Even if The Machine hadn't died, all the cameras he could see had the same problem: they were all dead. He would need to make it to a section where the cameras were working to see if he could get a message to someone.

The pain in his shoulder, stomach, and thigh returned with full vengeance, but he forced himself to keep moving as fast as he could. It wasn't fast enough. As he rounded a corner, he ran straight into the barrel of a gun. He heard men coming around behind him as well, and he knew he was stuck. He grudgingly held out his hands in surrender and the gun he had obtained was yanked from his hand. He looked past the gun sticking in his face and instead focused on the person who was wielding it.

"Control," he muttered darkly. She inclined her head.

"Mr. Reese." He stared at her as more men surrounded him.

"What is this about?" he asked. Instead of a reply, an arm wrapped around his neck and a needle was jammed into his artery. He felt a warm sensation spreading through his veins and his knees buckled under him. Strong arms caught him, and he felt someone grab him under the knees and armpits The last thing he heard before he lost the battle for consciousness was Control's voice.

"All in good time, John. All in good time."

The next time John woke up wasn't gradual at all. One minute he was blissfully unaware of what was going on around him, the next moment his eyes shot open and he tried to get out of the bed, eliciting an involuntary gasp of pain as he jostled his shoulder and side. His eyes darted over to his left side, noting that once again his arm had been strapped down at the wrist and elbow. His right arm was still in a sling, but he had a feeling they wouldn't be loosening that any time soon. He also noted that aside from his left arm being strapped down, they had wrapped a restraint over his chest, and had also taken his advice. Both of his legs were restrained at the ankles and knees.

The door opened and John couldn't help but smirk as the same doctor from before walked in. His nose was quite obviously broken and he glared at the ex-CIA agent. John was the first to break the silence this time.

"Hey doc, I can't feel my arm. Is there anything you can do to help?" He knew it was stupid to goad the man who was in charge of deciding how much of which drugs were given to him, but it was just so satisfying to see the look of fury intensify on the other man's face. The doctor leaned down close to John's face.

"You know what, there is something I can do," he sneered. He reached over and tightened the sling even more. John grunted as the pressure increased the pain in his shoulder, but he had been expecting something like that to happen.

"Dr. Murphy, you're excused," a harsh voice said from the doorway. Murphy gave John one last withering look before trading places with Control. She stared at the man in the bed for a second before speaking again. "You really shouldn't antagonize him, John. You never know what kind of drug cocktails he could mix up for you, and you would be powerless against him." John's face took on an impassive 'ask me if I care' look. Control looked at him with an equally uncaring look as she continued.

"It's been a little over a week since we pulled you off that roof top," she informed him. "I would think a 'thank you' would be appropriate."

"Thanks," John said quietly, obviously not meaning it. Control ignored his sarcasm. John had a thought. "I heard rumour you and Greer had a stand-off. He only recently died. How did you manage to get away from him before?" Control continued to stare at him with an unreadable expression.

"Your wounds were starting to heal, but then you had to go and pull out all the stitches and open the wounds again. You've lost a lot of blood over the past week and a half. It wouldn't be wise to lose any more," she cautioned. After a moment of debating, she decided to answer his last question. "As for Greer, he was going to kill me. However, a blackout at just the right moment was the distraction I needed. We both fired at each other as we were getting out of the building. He got me in the chest, but thanks to some very skilled doctors, I survived. And because I survived, you were able to be pulled off that roof."

"What is it you want?" he asked exasperatedly. He was done with this whole talk. If he was alive, there were people that he could be saving.

"Mr. Reese...John. We could really use a man of your skills for our team." He raised an eyebrow.

"You're offering me a job? You have a funny way of treating your potential employees," he commented, nodding his head at his restraints.

"They're for your own protection, Mr. Reese." He scoffed.

"Thanks, but I already have a job," he stated. She shook her head.

"Not anymore, you don't." He looked at her like she was crazy. She acknowledged his glance and continued to explain. "Your old job, saving people with Harold and Ms. Shaw. It no longer exists." John decided to play along.

"And why doesn't it exist anymore? Finch always has a way of doing the impossible. I'm sure we can find a way to continue saving people, even if The Machine is out of the picture." Control shook her head again.

"I'm afraid Harold and Ms. Shaw won't be doing much of anything anymore. They were both gunned down by Samaritan operatives before we could get to them." John stared at her, not believing the words he was hearing. "I'm sorry, John," she said as she placed her hand on the bed near his leg. He raised his eyebrows at her.

"Forgive me if I don't believe you. Both of them have been "dead" before."

"Why would I lie to you, John?"

"You just said it, you want me to come work for you. You think if I don't have anything to go back to with Harold, I'll decide that working for you is the next best thing." He shook his head. "Not working, sorry."

"I understand that this is difficult for you to take in right now. I'll come back later. Just think about what I said." She turned around and left the room, leaving John behind.


	3. Chapter 3

_A/N: OK hi guys. First of all, I didn't think anyone was actually going to read my stories, so when I saw the emails saying people had been reviewing it, I was shocked! Just as an FYI, the story is complete, I had just wanted to put out the first couple chapters and see what people thought! So by the end of today, maybe tomorrow morning, the full story should be posted! I just wanted to say thanks guys! I'll answer your comments when I can, thought I have to run to classes soon! Thanks again!_

 _BTW, I changed the time line in this story like a gazillion times, so I'm hoping I caught all the changes that needed to be made, but if I didn't, please feel free to let me know and I'll fix it!_

 _Present time, Finch & Shaw_

"Can you zoom in on the license plates on either of those vehicles?" Finch requested of The Machine. As the plate numbers became clear, Finch jotted them down. "Could you run the plate numbers and see to whom they belong?" As the AI started the process, Finch turned to the two women in the room with him. Shaw had a triumphant look in her eyes, and even Grace looked happy.

"I'm so happy for you, Harold," she said as she took his hands in hers. "John is alive!"

"Yes...or at least he was five weeks ago," he added. Shaw glared at him.

"We need an extraction strategy," she stated. Finch shook his head.

"I agree with you, Ms. Shaw, but until we know where he is being held, we cannot make any such plans. We would have nothing to go on, no idea what escape routes to take, nothing." Shaw's mouth slanted, but she knew he was right.

They sat in silence for a few minutes while they waited for The Machine to work through the databases trying to find out who the cars belonged to. Finally the monitor flashed, indicating The Machine had found something. All three of them leaned forward, looking at the findings. Harold tapped some keys on the keyboard, but after a few moments his shoulders slumped as he read what was on the screen.

"It's a shell corporation linked to an empty account. I can set up a program that can run the name and figure out who is behind it, but it will take time to program it, and then more time to let it run." The disappointment was clear on his face, and Grace leaned down and wrapped her arms around him from behind.

"No need," Shaw said with a cold look in her eyes. "That's ISA." Finch looked at her.

"Ms. Shaw, are you certain?"

"I worked with them for years, Harold. Pretty sure I know one of their fake corporations when I see one. Step aside. I know how to find where they're holding Reese."

 _July 15, 2016_

The door opened and John sighed in exasperation. It was Dr. Murphy, followed by six men armed to the teeth. "Well Mr. Reese, how are you feeling today?" The question was answered with silence, as it usually was.

The past few weeks had been a steady routine. The doctor would come in a few times a day, always guarded by ISA agents. They would let him up to use the bathroom, they would give him some food, ask him how he was doing, and then leave. John found out the hard way that if he tried to get away or fight at all, there was a stun gun with his name on it just waiting to be used. He hated being cooped up in the room, but he had to admit it; he was tired. After being shot multiple times by Samaritan ops, getting a concussion from the butt of a rifle, and the multiple encounters he had with the stun gun, he was simply tired. He also knew that they had given him sedatives. Not enough to knock him out usually, but just enough that he was more lethargic and couldn't fight back as well.

His wounds had actually healed quite well, but he still had the occasional twinge of pain whenever he moved a certain way. His shoulder had healed enough that they had removed his arm from the sling and promptly secured it to the bed via velcro as well.

The doctor continued checking John's charts while the men took up their usual positions by the door and by his bed. After a minute, Control walked into the room. John raised an eyebrow. She hadn't come in since last week, when she had thrown the pictures onto his bed.

 _Flashback to a week prior_

"John, I know this is hard to accept," Control said as she help up the pictures in front of him. He sat in stoic silence, looking her directly in the eyes and not at the photos in her hands. "But Harold and Shaw are dead." John didn't even dignify her with an answer. She sighed and rubbed her hand over her face. "Mr. Reese, the facts are in front of your eyes. One of the agents you disposed of on the roof got word to his friends before he died, telling them they had seen Harold leaving the roof of the building next to you. They met him at the bottom of the building. He never stood a chance. Ms. Shaw was with Detective Fusco when a Mr. Blackwell cornered them. Ms. Shaw was killed, and Detective Fusco has been in critical condition for a few weeks. He just got out of the hospital, and he took his son and they moved out of the city. You're alone, John." John took in a deep breath.

"You're wrong," he stated simply.

"Excuse me?"

"I. Don't. Believe. You." He enunciated every word. His eyes never left hers for a second.

"We have cold hard facts, Mr. Reese, I-"

"Photos can be faked," he interrupted. "Stories can be told, evidence can be manipulated."

"Mr. Reese, I-"

"No. You have tried to convince me that I failed in keeping everyone I love safe. I know what it feels like when you've failed to protect someone you love. I'm not feeling that now. So you can take your 'evidence' and leave me alone." Control had said nothing. She simply turned and left the room, taking the pictures with her.

 _End Flashback_

John stared at the woman as she walked towards him with a device in her hands. He thought about making a snarky remark, but decided she wasn't worth his time or energy. He shifted his gaze so he was staring blankly at the wall until she walked into his line of sight, forcing eye contact once again.

"Mr. Reese," she greeted. He gave no indication that he had heard her, so she just continued. "I think it's high time we let you out of those restraints for good, don't you?" He tilted his head.

"Does that mean you're admitting I was right and letting me go?"

"Heavens no. Call it a show of good faith. We need you in shape to go out on missions, which you won't be if you're tied down in bed. However," she continued as she held up the device in her hands; it almost looked like a gun. "There are a few stipulations." She walked to the side of his bed while fiddling with the instrument. Two men put their hands on John's shoulders to restrain him should he try to fight. He gave a slight wince as his almost-healed shoulder groaned under the new pressure. Control placed the device against John's right forearm and pulled a trigger. There was a sharp pain, but the only sign John showed that he felt it was a slow blink of his eyes. Control had a tissue and she wiped off the bit of blood that appeared on his arm before turning to the guards. "Release him." They all stood still, not wanting to untie the man who was obviously dangerous. "Do not make me repeat myself," she warned.

As the velcro straps being were undone, John simply sat there. As soon as the last strap was removed though, he burst into action. Or at least he tried to. He barely got one punch in before a terrible pain went up his arm and through his body. He collapsed to the ground with an agonized groan, holding his arm. Finally the pain subsided and he looked up at Control.

"I think you need to work on your definition of 'good faith,'" he muttered through his teeth. She stared impassively at him as she held up the gun-like instrument, not bothering to acknowledge his comment.

"You've just been injected with a state of the art tracking chip, complete with perimeter guard. I can see every move you make, watch you everywhere you go. If you go anywhere you're not supposed to, if you do anything I don't approve of, I can simply press this button and...well, you just experienced the low setting." John glared at her.

"You're no better than the Samaritan agents," he said with quiet rage. If you didn't know him, you'd think by the volume he spoke and the tone of his voice that he was just making small talk, but for those who knew him, those who knew what he was capable of knew that that tone of voice meant you should run the first chance you get. "You claim to be keeping the world safe, making it a better place, but at what cost? Imprisonment, torture, lying; the only thing that's different between you and Samaritan are your names." She blinked, then continued on like she hadn't heard him at all.

"The door to this room has been equipped with something akin an electric fence one would use to keep a dog in the yard, only it's got a bit more of a kick to it. If you manage to get past the door without collapsing, the electricity will only continue to increase in voltage. I think you can imagine what happens when it reaches full potential." Without saying another word, she turned and walked out the door, followed by everyone else in the room. The door shut, and John heard the electronic lock click into place. He rubbed his arm absentmindedly as he looked around, trying to find anything that would help him get out of his current situation.

 _July 16th, Present Time_

Over the course of the next 24 hours, John had tried every possible way he could think of to get out of his room, but every time he even went near the door, it would send a shock through his body. His arm was in an almost constant state of cramping now from the amount of times he had been shocked, and he was now sitting on the bed, giving his body a rest from the torture. He stared at the ceiling, trying to figure out how he could get out of here, or at least try to get a message to Finch. He sat that way for a few minutes before he heard the electronic lock being opened and in walked Control. She was holding a stack of clothes which she tossed to him. "Put these on," she ordered.

After he came out from the bathroom with his new clothes, Control beckoned him forward. "We're going on a walk," she informed him. He was skeptical and hung back. "Don't worry, you won't be shocked when you come near the door this time." Still, John didn't come forward. She sighed and motioned for two of the men who accompanied her to bring Reese with them as they walked out of the room. They walked behind John while two other men got in front of him, boxing him in. They marched out of the room like that with Control leading the way. They led him down a hallway and down a flight of stairs until they reached a door, which Control opened. John walked in and stared at the scene around him.

A series of walls had been set up strategically, and the room was dark. Reese realized what it was a split second before the door behind him closed. He was in a training room. A shot echoed around the room as something hard struck the wall right above his head. He instinctively ducked around the corner, pressing himself against the hard surface as he reached for his gun that was no longer at his side. He cursed and went into a crouch, staying low to the ground as he quickly made his way through the maze, never staying in one spot for more than a few seconds. He rounded one corner and came face to face with someone who raised a weapon at him. Almost without thought, John grabbed the gun and yanked on it, bringing the threat closer to him, then shoved the gun back in the face of the man, dropping him to the ground.

He grabbed the gun from the unconscious man, quickly patting him down for any other weapon that he could use but found nothing. He brought his newly-acquired rifle against his shoulder, keeping an eye out for anything that moved.

It was dark in the room, but his eyes adjusted quickly. He continued to creep around the corners, his breathing quiet and his senses on high alert. He was aware of almost every noise around him, every shifting of the shadows. He thought he saw something out of the corner of his eye, causing him to duck out of the path of a bullet just in time. It wasn't quick enough to avoid the bullet completely though. He hissed in pain as his left arm burned from the recent contact with the bullet. He turned and fired his own weapon, smiling a grim smile as he heard a cry of pain and a crash as the person who had shot at him fell. John could imagine them clutching at their leg in agony. He didn't know how many hostiles he was up against, but he knew there had to be more than two.

A few minutes passed with no action of any sort. As John made his way around one corner, he came to a sudden stop. Five men were standing there with weapons raised and aimed directly at him. His gun had automatically raised in defense, but he stopped and lowered it.

"I'm not playing your game anymore," he stated coldly. "If you want to have your men kill me, go ahead. I'm not going to work for you." He heard the shift of the guns as the men waited for orders.

He was expecting it, but he still fell to his knees as a stronger surge of electricity coursed through him. He fell against the wall after the currents stopped flowing, taking in deep breaths to try and even out his labored breathing. His arm was still spasming when a door was opened and Control stormed in. She barked at a few of the agents to go pick up the men John had taken out, while the rest of them stood behind her, waiting for a command. She stared at John, anger flashing in her eyes.

"Do your worst," John dared with a smile as he held his arm against his chest to try and control the shaking. She sat in silence a moment longer.

"Get him up," she finally ordered harshly. John was pulled to his feet, then dragged out into the hallway where they zip-tied his wrists together behind his back. Control stood in front of him. "You could have easily taken those men out back there," she pointed out. "Why didn't you?" John smirked.

"ISA needs all the help it can get," he replied simply. "I was only doing you a favor." Control said nothing, but jerked her head, indicating she wanted to start moving. They shuffled him down the hallway and got to the stairs, intending to take him back to his room to let him stew a few more days.

As they started going up the stairs, the lights flickered, then turned off all together. Flashlights were flipped on as they heard pounding steps coming down the stairwell and John was shoved against the wall as the fighting ensued. Through the searching flashlight beams, John could see that one of the ISA agents was standing in front of him, gun drawn and obviously trying to protect the prisoner. He knew he didn't have a lot of time, so as quickly as he could, he bent his knees and slipped his bound hands around his legs, bringing them to the front. He hit the man in the back of the head, knocking him to the ground instantly.

He turned and yanked the door open, running as fast as he could down the long hallway. He had just reached the end of the hallway and was about to turn the corner when the worst shock yet wracked it's way through his body. He couldn't stop the cry of pain that wrenched itself from his mouth as he fell to the floor, gripping his spasming arm. His momentum from running threw his falling body into the wall, dazing him. He felt hands grabbing him roughly, then heard a sickening slicing noise and pain exploded on his arm. He groaned in agony as he felt something digging around in his arm, but finally his body took mercy on him and he passed out.


	4. Chapter 4

"Got it!" Shaw said triumphantly, grabbing a pen and piece of paper to jot down the address.

"How were you able to-" Finch started, but Shaw cut him off.

"You learn a few things here and there. Maybe one day I'll show you!" She winked as she turned and started walking out of the warehouse. Harold turned and looked at Grace.

"Go!" she urged. "I'll be fine. I'll stay here and keep an eye on Bear," she promised. Finch gave her a loving smile and a quick peck on the cheek before turning and following Shaw out to their car. Shaw was already in the driver's seat, engine idling and waiting for the man to get inside. As soon as Harold was in the passenger seat, Shaw peeled out into the street, breaking almost every law known to drivers as she sped towards the address where John was being held.

Shaw threw the car into park as they reached the address she had found. It was an older looking building, but she knew that looks were deceiving, especially when it came to ISA. She hopped out of the driver's seat and immediately headed for the trunk while Finch got out of the passenger side. He walked to the trunk of the car and his eyes widened when he saw what was there.

No less than a dozen handguns, two sniper rifles, a set of knives, and he saw several flash-bang grenades littered the floor of the car's trunk. "Ms. Shaw…" he started. She stared at him.

"Do you wanna get John back or not?" Finch didn't say another word, silently giving her permission to do what she needed to get John back. She stuffed some of the grenades in her jacket pockets and grabbed two of the handguns, as well as several magazines before slamming the trunk. "Let's go," she said as they turned and headed for the building. As they neared one of the doors, Shaw turned to Finch.

"The Machine can't help us in there, she's completely blind. We're on our own, so you need to stay behind me," she insisted. Finch nodded, and she kicked the door in. She expected a hallway full of agents, but there were only two lonely figures. To say she was disappointed is an understatement. Those agents immediately started firing at them, but two carefully aimed shots incapacitated both of them. Shaw stalked up to them, getting down in their faces.

"Where is John?" she asked, deadly quiet. The agents only stared up at her with contempt written across their faces. She grabbed one of them by his bulletproof vest, pulling him up halfway off the floor. "I'm going to ask you again, and this time I want an answer. Where. Is. John. Reese?" She still received no response. "Do you know who I am?" she growled.

"Sameen Shaw," boomed a voice at the end of the hallway. Shaw immediately dropped the agent back to the ground, standing up and aiming her gun at the approaching figure. Her eyes narrowed even further as her suspicions were confirmed.

"Control," she hissed. "Give me one good reason why I don't put a bullet in your head right now!"

"I'll give you several. One: Harold there detests violence and I know he's had an affect on you."

"Right now, I think all Harold and I care about is getting our friend back," Shaw explained. Harold merely nodded his head. Normally, Control would be right, but they had had enough negative run-ins with her that, for the sake of John, he was willing to let Ms. Shaw try to scare her into telling them where their friend was.

"Two," Control continued after a moment of staring at the two of them. "I was the one who sent the team up on that roof to rescue John in the first place. Without me, he really would be dead." Shaw hated to admit it, but she did have a point. They wouldn't be here if it weren't for Control.

"Fine, maybe I won't kill you; but I won't lose any sleep at night by putting two bullets in your knees. But first you're going to take us to Reese," she demanded. Control shook her head.

"I would if I could. Unfortunately, Mr. Reese is no longer here," she confessed.

"What do you mean?" Harold asked, piping up for the first time since entering the building. Control switched her gaze to him and gave him a dead-looking stare.

"It means someone else knew he was still alive as well. We had a break-in just a few hours ago where several of my agents were severely injured. By the time the chaos settled down, John had disappeared."

"Take us to the last place you know he was at," Harold commanded, his voice firm, leaving no room for argument. Control simply turned and strode down the hallway she had come from and turned around a corner. Shaw and Finch followed as she led them down another hallway and down a flight of steps, through a door and to another long hallway. She gestured with her head.

"Down there." Shaw nudged her in the back with her gun, silently telling her that she wasn't allowed to stop moving yet. As they neared the indicated spot Finch's stomach dropped at what he saw. There was a pool of blood on the floor next to the wall. He turned to Control in anger.

"Who were they?" he demanded, advancing on the woman. She didn't budge as she stared at him with contempt.

"I don't know," she admitted. She absentmindedly fiddled with something in her pocket, which did not go unnoticed by Shaw.

"Empty your pockets," she ordered. Control gave her a look that said 'make me.' Shaw cocked her gun. "Or I could just shoot you now and forcibly remove whatever it is you're trying to hide?" Control continued glaring at the pair, but grudgingly she reached into her pocket and pulled out something small and bloody. Finch's eyes widened and he stared at Control with anger in his eyes.

"You chipped him?!" He grabbed it out of her hand and held it up to the light. He glared at the woman. "John would have tried to escape even if he knew he was being tracked, so something else stopped him. What else did this chip do?" When they received no answer, Shaw pressed the larger woman against the wall, noticing for the first time a large bruise forming on Control's temple.

"Answer the man's question." After a few more glares between the three of them, Control finally answered.

"It may have given him several... _shocking_ reasons to stay," she admitted.

"Electrocution?" Shaw's voice was dangerously quiet. Control was lucky Shaw didn't put a bullet in her right then, but she knew they still needed her. "So whoever it was that took him knew about the chip, meaning they somehow got in here beforehand. Who all knew about the chip?" Control stared for a minute longer, contemplating her options, then finally sighed.

"The only ones that knew about the chip were myself, John's doctor, and a half-dozen or so men."

"So it had to be one of those people. We need a list of everyone who knew about it, along with their addresses." Shaw let go of Control and motioned her forward. As they followed her to her office, Finch turned to his companion.

"We may need to call Detective Fusco for his help on this after all," he admitted.

"'Bout time," Shaw quipped quietly. Finch pulled out his phone as they entered the office. Control walked around to her computer to bring up the list Finch and Shaw were requesting while Finch held the phone up to his ear.

"Detective Fusco," came the gruff voice over the phone.

"Hello, Detective," Finch replied. There was silence on the other end. "Detective?" Finch pressed.

"It's been over a month, ya know that, right?" came the angry retort. "You couldn't even bother to let me know that you were alive? You'd better not be calling me just because you need my help with some number, because after the past month, I think I deserve more than just a 'Hello Detective, please can you risk your job again for us even though we didn't give you the courtesy of telling you we were alive?' I do have an actual job you know, and it's gotten pretty crazy around here! We just had-"

"Detective Fusco, I understand that you're upset, and you have every right to be. I just ask that you do one thing for us. We need your help in running down some addresses."

"This is about a number?!" Fusco exploded.

"Detective. I assure you this is more than just an ordinary number. The number we are looking for is Mr. Reese!" That statement was met with silence. "Detective? Are you still there?"

"Wonderboy's the number this time?"

"That is correct."

"I may have something that can help. I was trying to tell you earlier that we had a breakout about two hours ago," the detective explained.

"Who broke out?"

"All the remaining members of the brotherhood." Finch noticeably paled. If the brotherhood had Mr. Reese, he was truly in danger.


	5. Chapter 5

Reese jerked and sputtered awake as ice-cold water was splashed on him. He shook his head, spitting still as the water continued cascading down his face and into his mouth. He glanced up as he heard footsteps. He saw someone carrying a recently-emptied water bucket walking out of a door. He glanced around him, taking in his surroundings.

He was sitting on a chair in the middle of a large room. When he tried moving his legs, he found they were strapped to the legs of the chair. He glanced down at his arms, seeing that they were straight down, his wrists cinched to the back legs of the chair. As he was looking at his arms, he noticed his right arm had a bandage wrapped around it. There was a steadily-growing red spot in the center of it, and he remembered what happened right before he passed out. So he had been kidnapped from his original kidnappers. That was something that didn't happen every day.

The door to the room was slammed open again and he looked up to see who his most recent abductors were.

"Detective Riley," drawled a familiar voice. Walking towards him was Floyd, the only remaining high-ranking member of the Brotherhood. She stopped in front of him. "Or is it ' _Mr. Reese_ '?" He stayed silent, which earned him a backhanded slap. It was harder than he was anticipating; it snapped his head back and he tasted blood in his mouth. He slowly brought his head around to look at her again, not showing anything in his expression. She leaned down, putting her face close to his. "I am going to make you hurt," she promised. He quirked an eyebrow.

"You took the chip out of my arm," he commented. "I would think if you wanted to make me hurt, you would have left it in." She sneered.

"I could have, but it was also a tracking device; easily hacked. I remember your friend who was so good with computers. There was no way I was going to let him find us before I paid you back for what happened to Dominic."

"I wasn't responsible for what happened to him," Reese told her. She pulled out her gun and pistol-whipped him across his face faster than you could blink. He turned back to her, face still as unreadable as before, only now he had a long scratch that was rapidly swelling under his eye.

"He never would have been in that car had it not been for you!" she yelled. "If you had just left well enough alone, if you had let Elias and Dominic settle things their own ways, Dominic would still be here! But no, you had to go and be a hero."

"I'm not going to apologize for what I did," John informed her. "Elias was a bad man, but he had values; he had lines that he wasn't willing to cross. Dominic didn't care who got hurt as long as he got his way. If I had to choose between the lesser of the two evils, I would make the same choice again." Her eyes narrowed, and John expected more beatings, but instead she just turned and whistled. Three men walked in, and Reese recognized one of them as one of his guards from ISA. They stood around her and she smirked at John.

"There is also the matter of what Dominic was questioning you about last time you were together," she commented. She walked over to one of the walls and grabbed a folded chair that had been leaning against it. She brought it over and unfolded it a few feet away from her prisoner as her men stood around her. "Where is your friend?"

"What friend?" John asked in his quiet voice. She scoffed.

"Please, like a man like you would have that many friends. The one who called the shots. Your boss. Harold."

"I don't know." A nod from Floyd and the three men descended on John, punching everywhere they could: stomach, chest, face, even going for his wounded thigh. They finally pulled back, leaving John breathing heavily.

"I'm going to ask you again, and this time, I want the truth! Where is Harold?"

"I have no idea." She gave a frustrated laugh, scratching her head with the butt of her gun.

"I said I want the truth!"

"And I'm telling you the truth. I don't know where Harold is. They told me he was dead," he said, jerking his head toward the man who had posed as an ISA agent.

"Yeah, but you never believed them," the fake guard replied. John said nothing, and Floyd leaned down in his face again.

"We WILL get the information out of you, John. One way or another."

"Him," Finch said as they were going through the files of the people who knew about John's chip. "I recognize him from the time The Machine gave us the numbers of everyone in Elias's and Dominic's crew. This man worked for Dominic." Shaw grabbed the file out of Control's hand.

"Is this address good?" she asked the leader of ISA, who nodded her head.

"As far as we knew. When we checked it out, the landlord, his neighbors, and his background check all came back and said that he was someone we could count on in a tough situation." Shaw turned to Finch.

"Come on, we've got to go check this place out, see if it has any clues as to where they could have taken Reese. It wouldn't hurt to call Fusco for backup," she added. Finch nodded in agreement and pulled out his phone.

"Detective, thank you for coming," Finch said as they watched as Lionel get out of his car. Bear, whom Shaw had picked up on their way to the address of the gang member, whined as he saw Fusco walking towards them.

"Yeah, good to see you too, I'm fine, thanks for asking! I was only stabbed and thought you guys were dead, but hey! Nice to see some things never change," he groused.

"Detective please, if we could wait and hold this conversation until after we have John back?"

"Yeah yeah, alright. So this is where the guy who grabbed him lived?" The three of them stared up at the apartment.

"Yes. I have no idea what we'll find in there, but I'm hoping it will help us find John." They walked to the door of the landlord and knocked. When he opened the door, Fusco flashed his badge.

"NYPD sir. We just have a few questions regarding one of your residents?" The door opened wider.

"How can I help you?" Shaw held out a picture of the man.

"What can you tell us about him?" she asked.

"Mike? Good kid from what I could tell. Though he was always very secretive about what he was doing, where he was going."

"Did you ever notice anyone strange or tough looking that he would hang out with?" Fusco asked.

"Now that you mention it, there was a man just yesterday...or maybe it was the day before, I can't recall. But yes, the man that he was talking to did seem very shifty, not someone that I would allow to live here."

"May we see the apartment?" Finch asked. He was nervous. The longer they left John in the hands of the Brotherhood, the less chance they had of getting him back alive.

"Is Mike in trouble?" the landlord asked concernedly.

"We have it on good authority that the man you know as 'Mike' is actually named simply 'Ike,' and he belongs to the gang called the Brotherhood," Fusco explained. The landlord's eyes widened, and he immediately nodded his head and led them up the stairs to the apartment Ike had been renting.

"I thought that gang was broken up?"

"Yeah well they managed to piece themselves back together," Shaw said distractedly as she wandered around the apartment, looking for anything that could help them. Bear whined and pawed at a closet door. Finch opened it, and when the landlord saw the massive pile of drugs, his eyes widened in shock and surprise, as well as anger. Finch's mind started whirring as he looked around.

"Do you have a phone number for him?" The landlord nodded and hurried out the door to get the requested information.

"He won't have been dumb enough to keep the same phone on him now, if he even has one on him at all," Shaw pointed out.

"You're quite right, but if I can access the number, I can track where his GPS has been. We just need to find the most frequented place that would work to store this amount of drugs," he explained. The landlord came back in and handed Finch the paper with the number on it. Finch turned to the landlord. "Thank you, you have been a great help," he said with complete sincerity.

"Absolutely. Let me know if there's anything else I can do for you!" He walked out of the apartment, leaving the three friends and their dog alone in the apartment. Finch pulled out his phone and started typing away on it.

"I could really use some help," he muttered, knowing The Machine would be able to help him. Things on his phone started whizzing around as she accessed the cell phone and Finch looked at his companions. "It won't be long now," he promised.


	6. Chapter 6

_Okay all! This is the last chapter! Thank you thank you thank you so much for reading and reviewing! It means so much to me! Let me know what you think! Or don't...either way, hope you enjoyed my story!_

John's head hung down, chin touching his chest as he panted and tried to catch his breath. Blood dripped from his nose and mouth, and his eye was completely swollen shut. He was pretty sure he had felt a couple ribs crack, and all of his gunshot wounds had started throbbing and complaining an hour ago.

"Where do you guys meet?" Floyd asked for the umpteenth time. John simply closed his eyes and focused on his breathing, trying to even it out. "Where is Harold, Reese?" Still no reply. She let out a growl of frustration, pacing back and forth in front of him. Her leg suddenly lashed out and she kicked him square in the chest, forcing the hard-earned air out of his lungs and toppling his chair over backwards. He felt and heard a bone in his right arm crack as the chair plus his full body weight fell on his arm, and he barely kept in the cry of pain that tried to force it's way out of him. He closed his eyes and tried breathing through the pain.

"Just tell me what I want to know, John, and this can all end!" she promised, almost begging. Eyes still closed, John shook his head.

"You're never going to get what you want from me, so you might as well just end this right now," he replied. She contemplated him for a minute, then motioned to her men who hauled the chair back into its upright position. John winced as his broken arm was pulled on to get the chair in the proper place, but he hid his pain as Floyd faced him. She leveled her gun at him.

"You know what? I can tell you mean that," she conceded. "So while it's been fun, it's time to bring our talk to an end. This is for Dominic." John let out what he knew would be his final breath, ready to accept his fate. That is, until he heard a familiar voice.

"John!"

"This is the place your Machine thinks Reese is being kept?" Fusco asked skeptically.

"After running several tests and simulations based on what we know about the gang and what we found in Mr. Ike's apartment, yes. Ms. Shaw, now I believe would be a good time for that extraction strategy you were mentioning earlier today." Shaw nodded.

"Right. The Machine explained the layout to me and told me the best ways to get in without being spotted. Fusco, you need to take the back entrance and stick to the left side of the wall, in the shadows. I'm going in the side, which leads to a second floor. I'll have a good sniper shot there." She looked at Finch and Bear. "For now, until The Machine says otherwise, you need to stay out here," she instructed. Finch didn't like the idea of just sitting there, but he knew that it was the most logical way. He nodded reluctantly, and the other two took off, going towards their respective entrances.

After waiting for a few minutes, Harold's phone began to ring. He looked at the caller ID. Unknown. With slightly trembling fingers, he answered the call. "Hello?"

"Can you hear me?" Root's voice came in over the other end.

"I can," he affirmed, trying to control the sudden emotions he was feeling over hearing both his friend's and his Machine's voice again.

"I'd love to chat, but John is in danger," she informed him.

"We're aware of that, I thought that's why we're here?"

"It is, but Shaw and Detective Fusco aren't going to get to him in time. I need you to do exactly what I say and John has a slightly better chance of surviving."

"I understand. What do you need me to do?" Finch asked.

"Go to your left. There's a window right there. You need to get in the building through the window and immediately go down the hallway to your right." Finch followed these instructions, not even caring about the slight pain that his back was feeling as he got through the small window. He walked briskly down the hallway to his right, but before he had gone three paces, he heard a crash. "You need to hurry, Harold," The Machine urged him.

"Bear!" Finch whispered. The Malinois jumped through the window with ease and the two of them hurried to where the crash had come from.

"Stop." Finch did as The Machine commanded and waited for her to speak again. "It's the door to your left." Finch turned and twisted the handle, opening the door. The sight before him would forever haunt his dreams.

Mr. Reese, who Finch thought he would never see again, was bound to a chair, his face a bloody, swollen mess, but there was no mistaking the proud look on his friend's face. Standing in front of him was a woman whom Finch remembered as being sort of a confidant to Dominic. There were three other men surrounding the two of them, but they seemed more like the muscle; the woman seemed like she was in charge now. She said something to John and lowered her gun, pointing it directly at his friend's head. He stepped forward.

"John!"

Reese's head snapped up while the woman whirled around. She immediately went behind John and wrapped an arm around his neck, putting her gun to his head. She was crouched down behind the chair so that her body was fully hidden behind John's. One of the three men stood directly behind her, while the other two took up either side of her so she was completely blocked off.

"Who are you?" She called out. Harold was walking forward slowly, but the sound of the gun cocking stopped him cold. Bear growled, realizing his master was in danger, but Finch held a tight grip on his leash.

"I believe Dominic was also very interested to find out who I was," Harold supplied. Her eyes widened in surprise.

"You're the boss? The man behind everything?" She scoffed. "You don't seem like much."

"It's funny how so many times, the person you least expect to be something is actually the one with the most to hide," Harold mused. He started walking forward again.

"I swear if you come any closer, I'll pull this trigger," she warned as she tightened her hold on John's neck. His face was starting to turn a slightly darker shade of red, and Finch could see him struggling to get out from her grip.

"Please, I'll do what you want. Just let John go," Finch begged.

"Harold!" John choked out, glaring at his employer with his good eye. Floyd looked between the two of them.

"There's really no point in keeping the two of you alive now," she finally said. "I could never trust either of you to do what I would tell you to do. But thank you so much for making my job less difficult," she added as she smirked at Finch. "Now I don't have to track you down. You came to me!" She got closer to John's ear. "What do you think?" she whispered throatily. "Who should I kill first?"

"You don't need to kill Harold. He's done nothing to you, I'm the one that always stopped you guys!" John insisted. Floyd chuckled.

"So Harold first it is." She removed her gun from John's temple and aimed it at the bespectacled figure in front of her. The dog next to him was barking up a storm, but she would take care of him later. John struggled against her grip and Floyd swiftly hit him on the head with her gun, dazing him but not knocking him out. She wanted him to see his friend die. He groaned as he weakly strained against her still.

"Please," he whispered. She ignored him and started to pull the trigger. Before she finished though, there were other shots fired from both above and behind her. She stared in shock and anger as she watched her men fall around her, clutching their legs in agony. She barely had a chance to take in what was happening before she felt a searing pain in her side and she fell to the floor without a sound.

Finch let Bear go finally, and the dog raced over to his injured master. Fusco reached John the same time Finch did, with Shaw arriving as they were removing his restraints.

"What was that, Finch?!" Shaw practically yelled.

"The Machine informed me that you and Detective Fusco would not have made it in time to prevent this woman from shooting John!" Shaw didn't reply to that; she knew The Machine had a reason for everything it did. Besides, they had more urgent matters to attend to.

"Mr. Reese?" Finch asked quietly as he knelt down in front of his friend. He took in the sight of John as he was kneeling there. As he had noticed earlier, John's face was swollen, bruised, and cut, but now that Finch was closer, he could see that wasn't the only thing wrong. John's right arm was also swollen and discolored, and Finch knew that it was broken. That same arm also had a bandage with a massive red splotch in the middle that was slowly growing bigger. Those were only the visible injuries; he was sure Mr. Reese had other injuries that just weren't apparent at the moment.

"Finch...what are you doing here?" John asked in a husky whisper, his head struggling to stay up.

"We found out you were alive, and we couldn't not come find you, John!" Shaw cut the restraints off his arms, and he hissed as his broken arm was jostled.

"Here," Shaw said, stripping off her jacket, leaving only a tank-top underneath. She formed the jacket into a makeshift sling and tied it around John's neck. Bear was whining and trying to get his nose under John's left hand.

"Bear, Laat het met rust," Finch commanded. Bear immediately stopped, but his whimpering continued.

"It's fine, Finch," John muttered as they helped him up and put his good arm around Shaw's shoulder. Finch stayed on his other side with steadying hands. Reese swayed on his feet, only staying up because of the support from Finch and Shaw. Harold looked from Reese to the figures lying on the ground, then to the Detective. Fusco seemed to read his mind.

"Go, get Wonderboy outta here. I'll call this in and have someone come pick them up," he assured them.

"Thank you, Detective. For everything," Finch said. He really meant it. They owed the Detective more than they could ever pay back. Fusco nodded. Finch, Reese and Shaw started making their way slowly towards the door while Fusco pulled out his phone to make the call for backup. None of them noticed when Floyd quietly reached out for her fallen gun.

The Machine started to tell Shaw to look out, but a loud BANG echoed through the room before she could. The pressure on Harold and Shaw's shoulders increased as John grunted in pain and sagged between the two of them.

"NO!" Shaw yelled, turning, pulling her own gun and firing it at Floyd, hitting her square in the chest. She was dead before her hand with the gun hit the ground, but no one paid any attention to her. They were too busy watching the blood that was spreading across John's left side in horror. They laid him down and tried to stop the blood flow. Shaw pressed down on the wound hard to try and stop the bleeding, making John groan in pain. He had turned a deathly shade of gray, the strain of the last month apparent on his face. "Finch, go start the car," Shaw ordered. Finch was loathe to leave his friend, but he knew they needed help, so he got up and hurried out the door. "John? John, stay with me!" she said to her friend, applying more pressure on the wound. "We lost you once, Reese, we're not going to let you go again!" Bear was whimpering and nudging John's neck with his wet nose.

She wrapped John's left arm around her shoulders once again and hoisted him to his feet, struggling slightly under the dead weight of her friend. The Malinois stayed loyally by his master's side. Reese's head rolled on his shoulder. He was barely managing to stay conscious; the sweet unfeeling darkness was beckoning to him, and he just wanted to feel nothing. Fusco hurried over to the other members of the brotherhood, kicking their guns away and pulling out his pair of handcuffs, cuffing only one of them.

"Yo, you got any zip ties?" he called over to Shaw.

"Kinda busy here, Fusco!" she grunted. "Just stay there, make sure they don't move!" She staggered as her foot caught on a crack in the ground and John grunted. "Sorry, big guy," she whispered.

"Shaw, let me talk to him," The Machine said in her ear. Shaw reached up with her free hand and took her earpiece out of her ear, tilting John's head up so she could let him hear.

"John, someone wants to say hi," she said as she finally got the earpiece in. As soon as her hand was free, she wrapped it around John's waist to provide more support.

"Can you hear me?" John's eyes snapped open, dispelling the darkness for a moment.

"You're...you're here?" he asked, not sure if he believed his ears.

"I am. And people need you, John. The world needs you still, so you have to hang on!" John bobbed his head once.

"I'll try," he replied in a whisper. He and Shaw limped along, finally getting out the door. Finch had the car ready, engine running. He hopped out as he saw John and Shaw coming, opening the back door and helping ease John into the backseat. Bear jumped in and sat on the floor protectively.

"I'm driving, Finch," Shaw insisted. Harold gave her a look.

"Ms. Shaw, driving as you do with only me in the car is one thing, but Mr. Reese is seriously injured. I don't know if he could-"

"Finch, I know someone to take him to. So you can let me go exactly where I know we need to go, or you can try and follow my directions!" Finch hesitated for only a moment more before he finally nodded and sat in the passenger seat. He smelled burned rubber as Shaw raced off to find someone to help Mr. Reese.

"What's going on?!" cried the doctor. "I swear, I didn't say anything about the police to you!" Shaw dragged him along the corridor of the morgue and turned down another hallway, heading for one of the autopsy rooms. "I don't know anything about dead bodies," he added in a worried tone. Had she brought him here to kill him? He was on the verge of an all-out panic attack.

"Don't worry, that's not why I grabbed you out of your bed. If you had gone to the cops about me, believe me. I would know, and we wouldn't be having this conversation, because you would be dead." Her reluctant companion's eyes widened in fear.

"So why am I here? Are those men after me again?"

"Not everything is about you, doc!" she snapped exasperatedly. She finally opened the door to the room she was looking for and escorted the man inside. He stopped as he saw two men in the room. One had glasses and was standing next to a gurney, which held the second man. The second man obviously needed medical attention, and the doctor suddenly realized why he was here. "I need you to save this man's life," she explained as she went to stand by her friends. "And seeing as how I saved your life a few weeks ago, I figured it was only fair that you return the favor. I did what I could for him, but without the proper equipment, I wasn't able to fix everything. I can help you with whatever you need."

"Can you tell me what happened to him?" the doctor asked as he moved closer to his newest patient.

"Specifically? No. I can tell you he was beaten, electrocuted, has a broken arm and probably several broken ribs, and he was shot." The doctor's eyebrows had practically disappeared into his hairline as the list of injuries was recited.

"Looks like I've got my work cut out for me," he muttered to himself as he moved in closer to work on the injured man.

 _6 Days Later_

Control opened the door to her office and went to her desk. As she sat down, she addressed the woman in the dark corner. "Ms. Shaw, if you're here to ask me what I know about who has John, I can only tell you so many times that I don't know," she stated. Shaw walked forward silently.

"Don't worry, John's safe. We found who had him, and we took care of them. That's not why I'm here." Control looked up from her paperwork with a bored expression.

"Then to what do I owe the visit?"

"I just came to tell you that if you ever come near me or any of my friends again, I will kill you without a second thought."

"Ms. Shaw, you just threatened a federal agent. Need I tell you what the consequences for that are?"

"I may have threatened a federal agent, but I haven't done anything to you yet. You kidnapped a man and held him against his will for over a month. He told us you tried to convince him we were dead, so we can add psychological torture and manipulation to the list, and let's not forget the electrocution part," she hissed, placing her hands on the desk and leaning close to her old boss. "So, I'm telling you again. If you come near my friends and me, just remember. You hired me for my skills. You might want to remember which skills I excelled at." She pushed herself off the desk and strode out the door without another word.

"Hey partner," Fusco said as he walked into the group's latest base of operations. Bear was lying down next to John's bed, but he perked up when he saw the Detective walk in.

"Lionel," John greeted quietly. He tried to push himself up with his good arm, but Fusco hurried over.

"Whoa there buddy," he said. "No need to get up on my account." John hesitated for a moment, then finally leaned back against his pillows with a quiet grunt. "How ya feelin'?" Fusco asked.

"I'm fine," came the reply. Fusco rolled his eyes.

"You don't look fine," he pointed out.

"Then stop looking." Fusco chuckled.

"I'll deny it if you ever tell anyone I said this, but it's good to have you back," he confessed.

"I'm touched, Lionel," came John's dry-sounding reply.

"Yeah well, don't get used to it. I'm sure I'll be annoyed at you again before the day is out." John chuckled, eyes shutting in pain as the chuckling turned into a coughing fit, which wracked through his beaten body. Fusco looked at him with a concerned look in his eyes. "What did the doc say?"

"He said that Mr. Reese is very lucky that the infection that set in wasn't worse," Finch answered as he walked into the room with Grace by his side. "He also said he's lucky the electricity didn't do any permanent damage to his nerves in his arm. He might lose feeling every now and again for a while, but he should make a full recovery. If he stays in bed and RESTS!" He pointed the last part of that at John, stressing the last word especially.

"I take it he's not the best patient?" Fusco asked. "Why does that not surprise me?"

"I need to be doing something, Finch," John complained. "Sitting in bed was all I did for the past month!" Finch winced internally as he remembered what John told him about his time with Control and ISA. Finch thought for a minute, then finally decided to make a compromise.

"Will you promise not to do anything too physical? And by physical I mean running around, waving guns and throwing grenades at people?"

"You take all the fun out of life, Finch," John said jokingly. The door opened and Shaw strode in.

"Ah, Ms. Shaw. How is our number?"

"Safe. Made sure the ex wouldn't be coming after him again anytime soon. I also made a quick pit stop along the way, and Control should be out of our lives as well."

"Ms. Shaw, what did you-"

"Don't worry Harold. I didn't kill her. Just let her know I WOULD kill her if she came near us again." She looked pleased with herself, and everyone chuckled. Even Bear seemed to be smiling, tail wagging back and forth on the floor. Finch put his arm around Grace's shoulder, and she leaned against him.

John looked around at everyone around him. Just a few years ago he never would have considered these people his friends. He wished Carter and Root could be here, and even though things would never be the same as they were when those two were around, he had a feeling that things were going to be okay. The Machine was up and running, there were numbers still coming in, people needing to be saved, and he knew they would be able to make a small difference in the world. And in the end, it's usually the small differences that make the biggest changes.


End file.
